In my opinion, and don't take this as medical advice - I am not a qualified doctor - and if I were you, I would not take your daughter back.
When the nurse said, "the individual injections she had as a baby didn't 'count'", I think the nurse meant in terms of staff bonuses.
The GP surgery and its staff get ££,£££ of bonuses if they meet their immunisation targets, so of course, the nurse wants your daughter to return!
That's obviously it. Nothing to do with actually wanting children to stay healthy, is it? Oh no. And doctors are either stupid becuase they don't know that *insert quack remedy of choice* cures *insert ailment of choice*, despite it being all over the internet - especially here, on *insert quack-website-du-jour*, or, if they're not stupid, they must be actively suppressing it, because they don't get paid for *ludicrous quack remedy*. That's it! Conspiracy! Obviously. Sigh.